The complete mitochondrial DNA sequence of the Montecristo goat

•Contentious origins of the Montecristo goat isolate.•Sampled mitogenome belonging to domestic haplogroup A, indicative of feralization.•Coding variants shared with North Asian breeds.•Evidence for lineages with a palearctic distribution.

The remote island of Montecristo is renowned for a resident goat population, whose origins are unclear. We describe the complete mtDNA sequence of a male specimen captured on the island. The sequence turned out to belong to haplogroup (Hg) A. Our results exclude that the sequence belongs to a lineage more closely related to bezoars than domestic goats. The lineages most similar to the Montecristo sequence are currently found in Western Europe, favouring partial feralization for the Montecristo isolate. Positioning of the Montecristo mitogenome in the emerging phylogenetic tree for domestic goats reveals a new lineage with multiple derived nucleotide states shared with lineages so far described in Europe as well as in North Asian breeds. This reveals the presence, within Hg A, of lineages with a palearctic distribution, whose descendants are now grown from Eastern Asia to Western Europe.